normByRUVs {ribosomeProfilingQC} | R Documentation

## Normalization by RUVSeq

### Description

Normalization by RUVSeq:RUVs methods

### Usage

    normByRUVs(counts, RPFgroup, mRNAgroup = RPFgroup, k = 1)

### Arguments

`counts` | Output of countReads
`RPFgroup, mRNAgroup` | Groups for RPF and mRNA files
`k` | The number of factor of unwanted variation to be estimated from the data. See RUVs

### Value

Normalized counts list

### Examples

    ## Not run: ##waiting for EDASeq fix the issue.
    path <- system.file("extdata", package="ribosomeProfilingQC")
    #RPFs <- dir(path, "RPF.*?.[12].bam$", full.names=TRUE)
    #RNAs <- dir(path, "mRNA.*?.[12].bam$", full.names=TRUE)
    #gtf <- file.path(path, "Danio_rerio.GRCz10.91.chr1.gtf.gz")
    #cnts <- countReads(RPFs, RNAs, gtf, level="gene")
    cnts <- readRDS(file.path(path, "cnts.rds"))
    gp <- c("KD1", "KD1", "WT", "WT")
    norm <- normByRUVs(cnts, gp, gp)

    ## End(Not run)

[Package ribosomeProfilingQC version 0.99.9 Index]